Abstract
A genetic resource for studying genetic architecture of agronomic traits and environmental adaptation is essential for crop improvements. Here, we report the development of a rice nested association mapping population (aus-NAM) using 7 aus varieties as diversity donors and T65 as the common parent. Aus-NAM showed broad phenotypic variations. To test whether aus-NAM was useful for quantitative trait loci (QTL) mapping, known flowering genes (Ehd1, Hd1, and Ghd7) in rice were characterized using single-family QTL mapping, joint QTL mapping, and the methods based on genome-wide association study (GWAS). Ehd1 was detected in all the seven families and all the methods. On the other hand, Hd1 and Ghd7 were detected in some families, and joint QTL mapping and GWAS-based methods resulted in weaker and uncertain peaks. Overall, the high allelic variations in aus-NAM provide a valuable genetic resource for the rice community.
Highlights
Improvement of rice (Oryza sativa L.) production has been achieved by development of new varieties and optimization of cultural practices
We describe the development of a rice nested association mapping (NAM) population using aus varieties as diversity donors and test its quantitative trait loci (QTL) mapping powers using known flowering-time genes
We developed and characterized the first rice NAM population using the aus varietal group as diversity donors
Summary
Improvement of rice (Oryza sativa L.) production has been achieved by development of new varieties and optimization of cultural practices. Genome sequencing has enhanced identification of causal genes related to yield [2] Most of these genes/QTL were identified using bi-parental populations, combined with the development of backcrossed progeny [3]. Development of next-generation sequencing (NGS) technology enabled direct detection of genetic loci associated with traits through genome-wide association studies (GWAS) [4]. GWAS can utilize a variety of germplasm collections such as landraces, breeding lines, and varieties that have accumulated recombination events both recent and historic This attribute gives GWAS a higher gene mapping resolution compared with bi-parental populations [5,6,7]. We describe the development of a rice NAM population using aus varieties as diversity donors (aus-NAM) and test its QTL mapping powers using known flowering-time genes. For GWAS, parental DNA variants were projected onto the progeny genotypes, and mapping of days to heading (DTH) QTL/genes was performed
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